Yes i am having the same problem but my only way of thinking round this, is to wait maybe a day or two because Call Of Duty Black Ops II had the same problem but with the clan tags in game but because cod has never had a in game version to run a clan, this maybe the same problem as Black Ops II but with a clan. And if that still doesn't work then i would suggest checking if they are already in a clan, and also i have realized that the people who have never had cod elite and sign up to it via game on COD Ghosts menu show up on the rooster fine? Please tell me if this helps!
This is a known issue that is occuring where people are somehow in 2 different clans. The app recognizes them as being in one clan and the game recognizes them as being in another clan. See #17 in the thread below: